Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1

From: Santanu Santra (santop420_at_gmail.com)
Date: Sun Feb 02 2020 - 22:04:18 CST

The error is coming for every lone pairs :::

Another error log is
==========================

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A
LPDO1 (ATOMS 8 9 11)

Charm++ fatal error:
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 (ATOMS
8 9 11)

Aborted (core dumped)
======================================
thanks for any help
santanu santra

On Mon, Feb 3, 2020 at 9:30 AM Santanu Santra <santop420_at_gmail.com> wrote:

>
>
> Hi everyone,
> I tried to model one model protein in drude forcefield
> (toppar_drude_master_protein_2013f.str) and successfully generated the
> structure by psfgen. But when I am trying to minimize it in namd, it is
> showing some error throwing message of "unable to find the angle parameter
> for lone pairs and two other atoms". I checked the ANGLE section in the
> *.str file to find the combination of these three atoms but it was not
> there.
>
> Can anyone please suggest me where from I can get the Ktheta and
> Theta0values for those angles including lone pair as one of these three
> atoms.
>
> Exact error log is ::::
> =====================================================
>
>
>
>
>
>
> *------------- Processor 0 Exiting: Called CmiAbort ------------Reason:
> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR LPD OD2C1A LPD (ATOMS 91
> 87 92)Charm++ fatal error:FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR
> LPD OD2C1A LPD (ATOMS 91 87 92)Aborted (core dumped)*
> *==================================================*
>
> The section of pdb for which it is throwing error is as follows :
> ================================================
> ATOM 8 C GLY 1 -2.504 6.616 3.758 1.00 0.00
> XXX C
> ATOM 9 O GLY 1 -1.357 7.045 3.786 1.00 0.00
> XXX O
> ATOM 10 LPOA GLY 1 -0.585 6.409 3.797 0.00 0.00
> XXX H
> ATOM 11 LPOB GLY 1 -1.192 8.031 3.797 0.00 0.00
> XXX H
> ===========================================================
>
> Any kind of suggestion is highly accepted.
>
> Thanks and regards
>
> Santanu Santra
>
>

-- 
Santanu Santra
Research Scholar
Molecular Simulation Laboratory
Department of Chemistry
NIT ROURKELA
ROURKELA, 769008

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